Yes, it seems such an obvious gap. You can import books from Calibre, you can assign tags manually, but it doesn't import tags from Calibre, despite the OPDS browser showing them. The best you do at the moment is import all books for a given tag, then manually assign them all in ShuBook, then move onto the next tag. That wouldn't work if you had more than one tag per book.

There is no way I would manually tag books that have already been tagged in Calibre just so that they can show up in categories on the device. This is why Android has a much better group of reading apps than iOS ...

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Hmm, I don't really see that, to be honest. I use BlueFire reader, and might now try ShuBook, on iOS, I use Moon+ on Android. They each do what I want of them, I find the iOS ones a bit slicker.
But then I have a reasonably small set of requirements.

In Android, there are at least 3 apps that will recognize the tags that were added via Calibre and automatically show your books in collections -- FBReader and Mantano plus Calibre Companion, a library management app.

Android also has many other full-featured reading apps such as Aldiko, Moon reader, and Cool reader. Some of these apps even have text-to-speech options.

Those 6 Android apps alone as a group are far more than what you can find on iOS, where currently only Shubook can be considered full-featured and current with iOS 6. And I don't know of a single iOS app that will read Calibre tags and group your books into collections with the exception of Stanza which is now broken on iOS 6.

Yes, there are options on iOS, but overall they pale in comparison to Android.